Datasets:

junidude14
/

PBISC-data

+{
+ "schema_version": "pbisc_sdd.utility6k.refcal_refs.train_distribution_reference.v1",
+ "written_utc": "2026-09-26T14:17:04.373563+00:00",
+ "tool": {
+  "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/refcal_refs/tools/build_train_reference.py",
+  "sha256": "3974eab839b323b9712653d6369e075fb2ed0e977f7e9fabb670a7993a53974b"
+ },
+ "inputs": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/ordered_train_recipes.csv": "7c3aadcc409c685605f0f610a0dcc48b1ee5e126dcd80b427e835d1e598e5a3a",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/manifest.json": "acbc8bc2cca5ecf3d3002e711b1d4a55b4069f17ae9666f0d64c197ca5cbc775",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/effective_config.json": "0a8e9a0ce0b82d136d3e439cbca6d6d61ed7f6b8a8f935cedd69d8c65fb15abd",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/EPOCH_SCHEDULE.json": "ae4e69c2181a420cab62078b999327991d575459e5ef97de0af7895512ad8b16",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/full_recipe_allcells_6k_broad_20260909/topup_v1/topup_recipes.csv": "ad94944067f1697e6a6f7d33b82a0fecbc63e271af25448d712cd5de69a7d700",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/full_recipe_allcells_6k_broad_20260909/topup_v1/manifest.json": "df300a6f7f758c865209c6640e51abcbec10bab9726ee48c3bc3434936316da1",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-000.parquet": "bdc1875f34f9754d94750e0d968b83f33efc01cbae9d967032fc5ed97de43c36",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-001.parquet": "be0d8fa3d85de56eddedcd77370de3427ed6a1e7fd27830b550650ab4b43633c",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-002.parquet": "9022f271e2a291c1cbf979d45911e89908faaf00334ef586e92949a5fe346fb5",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-003.parquet": "cc2bd2b099ef2d48c8ff3992bb219692a18a3bcd2b8f67aa2edb0165fba2c136",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-004.parquet": "535c5c9e8f7a2317d593e8e03c677c4cc1fb233b0bd70a9159d534d4d01e4814",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-005.parquet": "af8b8dd9e529ba5e1ff38b0c1105de2fa581c684c0b245a2b00db8d3cb61c405",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-006.parquet": "3a6e6731a3284f389f50713eb42a64b6cf64526a78631c036ec663ebb542bfa2",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-007.parquet": "65fb7c3933e4a077bb1876e37f85f63297c995ecb20cb62f9240598aac118672",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-008.parquet": "802567424fedff8f4038ab9cfe4b886eb25a3ac490c36a43f7ab7f3607dff115",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-009.parquet": "ba38b56f0ad98e853753d58fa521183977b2ab0bb5fddc1d7d1f73f0a6f9f317",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-010.parquet": "f2956bdec0a88e44c12bcbdee63d8e1d7412e4b40e942d06f0350d5dd4a5f400",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-011.parquet": "1e893d164e32ada346d6b5068821011677f29d60fbf2965976d9722c5ac5f649",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-012.parquet": "ddbe429b657b3b6b1cf474c417155c5a00f7009f2e6660079aa6517b4a35a518",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-013.parquet": "ad43faa41a805c035b8e91f0b6e69b01e4365f70b422c522e2dee8d4d047ba33",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-014.parquet": "0254004bdc0bc84e2936d5f2a082fd78a5c6453adc823dcbeffbca8a7ef09548",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/recipes/train-slot-015.parquet": "bac7d8c39ab864ebd658844bbbcbb28a6701ef15dc1e0a2ec747983c3bdaa1e3",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/metadata/sample_index.parquet": "8c4b38d313eac651f545979ef5813c60fa47ff59da8c07f11e1712b8a83d2322",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/metadata/sample_pools.parquet": "5f272fba92c0b388a3d7cd27f1fcb5ccd3e7edb5490c95948a50bc2ba35da8d1",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/metadata/source_shards.parquet": "14c9befabe3c901613321682d8a1b3be0de5182613265584ee6baea2e6badf28",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_source/metadata/var.parquet": "64f4e30e17763bef37793e7229edb6caa0a7ffe3f3bfa5a08e1d4ca8ea7ea1dc",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_source/BUILD_COMPLETE.json": "1eda0f644800400cf3547327252fb8d3c8f95d7e606623bf89ab695c64225127",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_source/dataset_manifest.json": "c37592be1f7951443551645fd86081e05f5515d6c25d51bdfaedf2f08c5f5fb7"
+ },
+ "corpus": {
+  "e2_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_source",
+  "e2_index": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index",
+  "build": {
+   "base_source_root": "/home/sj_server_1/PBISC/PBISC-data/single-cell-data-block-blood",
+   "dataset_manifest_sha256": "c37592be1f7951443551645fd86081e05f5515d6c25d51bdfaedf2f08c5f5fb7",
+   "gene_panel_sha256": "64f4e30e17763bef37793e7229edb6caa0a7ffe3f3bfa5a08e1d4ca8ea7ea1dc",
+   "logical_cells": 41395184,
+   "n_datasets": 22,
+   "schema_version": "model7.e2_strict_source.v1",
+   "source_fingerprint_sha256": "653a06a72a2a785bc2e21fe1666950319e21847dd382e7ff7bfc852815a5f58f",
+   "status": "complete"
+  },
+  "shards_read": 384,
+  "train_samples": 5232,
+  "train_pool_cells": 33141380,
+  "cell_cap_per_sample": null,
+  "counts": "raw UMI counts of the corpus Zarr shards, canonical 20,097 axis, every train-pool cell"
+ },
+ "value_sum_is_log_scale": {
+  "binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/sufficient_statistics/binding.json",
+  "collector": "pbisc_sdd.panel_ladder.collect_train_panel_statistics: value_sum += sum of log1p(x / cell total * target_sum)",
+  "target_sum": 10000.0,
+  "consequence": "a mean of log-normalised values cannot give a mean CPM; per-sample raw-count pseudobulks used instead"
+ },
+ "schedule_check": {
+  "ordered_train_recipes_equal_train_slot_000": true,
+  "ordered_train_recipes_in_epoch1_schedule": 1.0,
+  "epoch1_first_ids_equal_ordered_order": true,
+  "epochs": 16,
+  "scheduled_recipes_all_epochs": 134730,
+  "distinct_scheduled_recipes": 134730,
+  "slot_recipes": 131072,
+  "topup_recipes": 3658,
+  "scheduled_target_cells_all_epochs": 195639930
+ },
+ "evaluation_cohorts_excluded": {
+  "evaluation_accessions": {
+   "ImMicro": [
+    "GSE314416",
+    "GSE314922"
+   ],
+   "Randolph": [
+    "GSE162632"
+   ],
+   "Arunachalam": [
+    "GSE152418",
+    "GSE155673"
+   ],
+   "Behcet": [
+    "GSE198533",
+    "GSE198616"
+   ]
+  },
+  "provenance_files": {
+   "ImMicro": [
+    "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/analyses/offset_sample_size_20260914/features.json"
+   ],
+   "Randolph": [
+    "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/analyses/offset_two_cohort_20260915/paired_features/FEATURES_PROVENANCE.json"
+   ],
+   "Arunachalam": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/conditions/MANIFEST.json"
+   ],
+   "Behcet": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_repro_20260921/conditions/MANIFEST.json",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/conditions_more/MANIFEST.json"
+   ]
+  },
+  "training_corpus_dataset_ids": [
+   "001_A_collection_436154da-bcf1-4130-9c8b-120ff9a888_Perez_et_al._lupus_PBMC_cell-type-specific_molecular_genetic_associations_to_lup",
+   "005_A_collection_dde06e0f-ab3b-46be-96a2-a8082383c4_OneK1K_Yazar_et_al._single-cell_eQTL_mapping",
+   "006_A_collection_ced320a1-29f3-47c1-a735-513c7084d5_AIDA_Asian_Immune_Diversity_Atlas",
+   "007_A_collection_e1a9ca56-f2ee-435d-980a-4f49ab7a95_Miao_et_al._RA_PBMC_disease_activity-associated_PBMC_subsets",
+   "009_A_Human_Immune_Health_Atlas_Human_Immune_Health_Atlas_AIFI_immune_dynamics_across_healthy_age",
+   "010_A_collection_4a9fd4d7-d870-4265-89a5-ad51ab811d_ScaleBio_single-cell_RNA_sequencing_of_human_PBMCs",
+   "053_B_collection_b0cf0afa-ec40-4d65-b570-ed4ceacc68_Integrated_analysis_of_multimodal_single-cell_data_CITE-seq_PBMC",
+   "058_B_collection_eb735cc9-d0a7-48fa-b255-db726bf365_COVID_PBMC_nasal_swab_donors_with_immunodeficiencies_and_autoimmune_conditions",
+   "061_A_GSE274680_Savage_Allen_RA_at-risk_longitudinal_progression_PBMC_multi-omic_cohort",
+   "065_A_GSE271896_GSE271896_Sound_Life_deep_longitudinal_immune_profiling",
+   "071_C_JDM_CITE-seq_PBMC_CELLxGENE_JDM_CITE-seq_PBMC_CELLxGENE",
+   "074_A_COMBAT_CELLxGENE_collection_COMBAT_CELLxGENE_collection",
+   "081_B_Single-cell_atlas_of_peripheral_immune_respon_Single-cell_atlas_of_peripheral_immune_response_to_SARS-CoV-2",
+   "093_C_Local_and_systemic_SARS-CoV-2_response_CELLxG_Local_and_systemic_SARS-CoV-2_response_CELLxGENE",
+   "200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling",
+   "202_B_GSE161918_Time-resolved_Systems_Immunology_Reveals_a_Late_Juncture_Linked_to_Fatal_COVID-1",
+   "203_B_CELLxGENE_665714af_Ancestral_and_environmental_diversity_shape_the_immune_landscape_in_Indonesia",
+   "204_B_CELLxGENE_cHSPC_aging_MDS_Human_circulating_hematopoietic_stem_and_progenitor_cells_in_aging_cytopenia_and",
+   "300b_A_GSE132802_DRESS_DiHS_PBMC_only_scRNAseq",
+   "301_A_GSE163121_SLE_healthy_Bcell_PBMC_scRNAseq",
+   "302_A_GSE314010_SLE_IL36_stim_PBMC_scRNAseq",
+   "304_A_Parse_10M_PBMC_12donor_90cytokines"
+  ],
+  "training_corpus_accessions": [
+   "GSE132802",
+   "GSE161918",
+   "GSE163121",
+   "GSE271896",
+   "GSE274680",
+   "GSE275067",
+   "GSE314010"
+  ],
+  "hits": {
+   "ImMicro": [],
+   "Randolph": [],
+   "Arunachalam": [],
+   "Behcet": []
+  },
+  "paired_datalake_in_corpus_manifest": false,
+  "none_in_training_corpus": true
+ },
+ "variants": [
+  "recipes_epoch1",
+  "recipes_all_epochs",
+  "cells_all_epochs",
+  "samples_equal"
+ ],
+ "primary_variant": "recipes_epoch1",
+ "weighted_samples": {
+  "recipes_epoch1": 2853,
+  "recipes_all_epochs": 5232,
+  "cells_all_epochs": 5232,
+  "samples_equal": 5232
+ },
+ "dataset_share_of_weight": {
+  "recipes_epoch1": {
+   "001_A_collection_436154da-bcf1-4130-9c8b-120ff9a888_Perez_et_al._lupus_PBMC_cell-type-specific_molecular_genetic_associations_to_lup": 0.0166,
+   "005_A_collection_dde06e0f-ab3b-46be-96a2-a8082383c4_OneK1K_Yazar_et_al._single-cell_eQTL_mapping": 0.02258,
+   "006_A_collection_ced320a1-29f3-47c1-a735-513c7084d5_AIDA_Asian_Immune_Diversity_Atlas": 0.03064,
+   "007_A_collection_e1a9ca56-f2ee-435d-980a-4f49ab7a95_Miao_et_al._RA_PBMC_disease_activity-associated_PBMC_subsets": 0.01062,
+   "009_A_Human_Immune_Health_Atlas_Human_Immune_Health_Atlas_AIFI_immune_dynamics_across_healthy_age": 0.04614,
+   "010_A_collection_4a9fd4d7-d870-4265-89a5-ad51ab811d_ScaleBio_single-cell_RNA_sequencing_of_human_PBMCs": 0.08521,
+   "053_B_collection_b0cf0afa-ec40-4d65-b570-ed4ceacc68_Integrated_analysis_of_multimodal_single-cell_data_CITE-seq_PBMC": 0.01294,
+   "058_B_collection_eb735cc9-d0a7-48fa-b255-db726bf365_COVID_PBMC_nasal_swab_donors_with_immunodeficiencies_and_autoimmune_conditions": 0.01172,
+   "061_A_GSE274680_Savage_Allen_RA_at-risk_longitudinal_progression_PBMC_multi-omic_cohort": 0.06702,
+   "065_A_GSE271896_GSE271896_Sound_Life_deep_longitudinal_immune_profiling": 0.12842,
+   "071_C_JDM_CITE-seq_PBMC_CELLxGENE_JDM_CITE-seq_PBMC_CELLxGENE": 0.00781,
+   "074_A_COMBAT_CELLxGENE_collection_COMBAT_CELLxGENE_collection": 0.03088,
+   "081_B_Single-cell_atlas_of_peripheral_immune_respon_Single-cell_atlas_of_peripheral_immune_response_to_SARS-CoV-2": 0.02173,
+   "093_C_Local_and_systemic_SARS-CoV-2_response_CELLxG_Local_and_systemic_SARS-CoV-2_response_CELLxGENE": 0.01953,
+   "200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling": 0.0675,
+   "202_B_GSE161918_Time-resolved_Systems_Immunology_Reveals_a_Late_Juncture_Linked_to_Fatal_COVID-1": 0.02368,
+   "203_B_CELLxGENE_665714af_Ancestral_and_environmental_diversity_shape_the_immune_landscape_in_Indonesia": 0.02087,
+   "204_B_CELLxGENE_cHSPC_aging_MDS_Human_circulating_hematopoietic_stem_and_progenitor_cells_in_aging_cytopenia_and": 0.03613,
+   "300b_A_GSE132802_DRESS_DiHS_PBMC_only_scRNAseq": 0.00647,
+   "301_A_GSE163121_SLE_healthy_Bcell_PBMC_scRNAseq": 0.00549,
+   "302_A_GSE314010_SLE_IL36_stim_PBMC_scRNAseq": 0.00757,
+   "304_A_Parse_10M_PBMC_12donor_90cytokines": 0.32043
+  },
+  "recipes_all_epochs": {
+   "001_A_collection_436154da-bcf1-4130-9c8b-120ff9a888_Perez_et_al._lupus_PBMC_cell-type-specific_molecular_genetic_associations_to_lup": 0.02478,
+   "005_A_collection_dde06e0f-ab3b-46be-96a2-a8082383c4_OneK1K_Yazar_et_al._single-cell_eQTL_mapping": 0.02699,
+   "006_A_collection_ced320a1-29f3-47c1-a735-513c7084d5_AIDA_Asian_Immune_Diversity_Atlas": 0.03365,
+   "007_A_collection_e1a9ca56-f2ee-435d-980a-4f49ab7a95_Miao_et_al._RA_PBMC_disease_activity-associated_PBMC_subsets": 0.00996,
+   "009_A_Human_Immune_Health_Atlas_Human_Immune_Health_Atlas_AIFI_immune_dynamics_across_healthy_age": 0.04595,
+   "010_A_collection_4a9fd4d7-d870-4265-89a5-ad51ab811d_ScaleBio_single-cell_RNA_sequencing_of_human_PBMCs": 0.08289,
+   "053_B_collection_b0cf0afa-ec40-4d65-b570-ed4ceacc68_Integrated_analysis_of_multimodal_single-cell_data_CITE-seq_PBMC": 0.01277,
+   "058_B_collection_eb735cc9-d0a7-48fa-b255-db726bf365_COVID_PBMC_nasal_swab_donors_with_immunodeficiencies_and_autoimmune_conditions": 0.01002,
+   "061_A_GSE274680_Savage_Allen_RA_at-risk_longitudinal_progression_PBMC_multi-omic_cohort": 0.06872,
+   "065_A_GSE271896_GSE271896_Sound_Life_deep_longitudinal_immune_profiling": 0.13248,
+   "071_C_JDM_CITE-seq_PBMC_CELLxGENE_JDM_CITE-seq_PBMC_CELLxGENE": 0.00729,
+   "074_A_COMBAT_CELLxGENE_collection_COMBAT_CELLxGENE_collection": 0.03062,
+   "081_B_Single-cell_atlas_of_peripheral_immune_respon_Single-cell_atlas_of_peripheral_immune_response_to_SARS-CoV-2": 0.02114,
+   "093_C_Local_and_systemic_SARS-CoV-2_response_CELLxG_Local_and_systemic_SARS-CoV-2_response_CELLxGENE": 0.02105,
+   "200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling": 0.06677,
+   "202_B_GSE161918_Time-resolved_Systems_Immunology_Reveals_a_Late_Juncture_Linked_to_Fatal_COVID-1": 0.01973,
+   "203_B_CELLxGENE_665714af_Ancestral_and_environmental_diversity_shape_the_immune_landscape_in_Indonesia": 0.02003,
+   "204_B_CELLxGENE_cHSPC_aging_MDS_Human_circulating_hematopoietic_stem_and_progenitor_cells_in_aging_cytopenia_and": 0.03396,
+   "300b_A_GSE132802_DRESS_DiHS_PBMC_only_scRNAseq": 0.00507,
+   "301_A_GSE163121_SLE_healthy_Bcell_PBMC_scRNAseq": 0.00477,
+   "302_A_GSE314010_SLE_IL36_stim_PBMC_scRNAseq": 0.00719,
+   "304_A_Parse_10M_PBMC_12donor_90cytokines": 0.31418
+  },
+  "cells_all_epochs": {
+   "001_A_collection_436154da-bcf1-4130-9c8b-120ff9a888_Perez_et_al._lupus_PBMC_cell-type-specific_molecular_genetic_associations_to_lup": 0.0113,
+   "005_A_collection_dde06e0f-ab3b-46be-96a2-a8082383c4_OneK1K_Yazar_et_al._single-cell_eQTL_mapping": 0.0142,
+   "006_A_collection_ced320a1-29f3-47c1-a735-513c7084d5_AIDA_Asian_Immune_Diversity_Atlas": 0.02795,
+   "007_A_collection_e1a9ca56-f2ee-435d-980a-4f49ab7a95_Miao_et_al._RA_PBMC_disease_activity-associated_PBMC_subsets": 0.00979,
+   "009_A_Human_Immune_Health_Atlas_Human_Immune_Health_Atlas_AIFI_immune_dynamics_across_healthy_age": 0.0486,
+   "010_A_collection_4a9fd4d7-d870-4265-89a5-ad51ab811d_ScaleBio_single-cell_RNA_sequencing_of_human_PBMCs": 0.08407,
+   "053_B_collection_b0cf0afa-ec40-4d65-b570-ed4ceacc68_Integrated_analysis_of_multimodal_single-cell_data_CITE-seq_PBMC": 0.0135,
+   "058_B_collection_eb735cc9-d0a7-48fa-b255-db726bf365_COVID_PBMC_nasal_swab_donors_with_immunodeficiencies_and_autoimmune_conditions": 0.01039,
+   "061_A_GSE274680_Savage_Allen_RA_at-risk_longitudinal_progression_PBMC_multi-omic_cohort": 0.07322,
+   "065_A_GSE271896_GSE271896_Sound_Life_deep_longitudinal_immune_profiling": 0.1447,
+   "071_C_JDM_CITE-seq_PBMC_CELLxGENE_JDM_CITE-seq_PBMC_CELLxGENE": 0.00606,
+   "074_A_COMBAT_CELLxGENE_collection_COMBAT_CELLxGENE_collection": 0.0323,
+   "081_B_Single-cell_atlas_of_peripheral_immune_respon_Single-cell_atlas_of_peripheral_immune_response_to_SARS-CoV-2": 0.02192,
+   "093_C_Local_and_systemic_SARS-CoV-2_response_CELLxG_Local_and_systemic_SARS-CoV-2_response_CELLxGENE": 0.02224,
+   "200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling": 0.07175,
+   "202_B_GSE161918_Time-resolved_Systems_Immunology_Reveals_a_Late_Juncture_Linked_to_Fatal_COVID-1": 0.02035,
+   "203_B_CELLxGENE_665714af_Ancestral_and_environmental_diversity_shape_the_immune_landscape_in_Indonesia": 0.01754,
+   "204_B_CELLxGENE_cHSPC_aging_MDS_Human_circulating_hematopoietic_stem_and_progenitor_cells_in_aging_cytopenia_and": 0.03514,
+   "300b_A_GSE132802_DRESS_DiHS_PBMC_only_scRNAseq": 0.00513,
+   "301_A_GSE163121_SLE_healthy_Bcell_PBMC_scRNAseq": 0.0049,
+   "302_A_GSE314010_SLE_IL36_stim_PBMC_scRNAseq": 0.00782,
+   "304_A_Parse_10M_PBMC_12donor_90cytokines": 0.31714
+  },
+  "samples_equal": {
+   "001_A_collection_436154da-bcf1-4130-9c8b-120ff9a888_Perez_et_al._lupus_PBMC_cell-type-specific_molecular_genetic_associations_to_lup": 0.20967,
+   "005_A_collection_dde06e0f-ab3b-46be-96a2-a8082383c4_OneK1K_Yazar_et_al._single-cell_eQTL_mapping": 0.15004,
+   "006_A_collection_ced320a1-29f3-47c1-a735-513c7084d5_AIDA_Asian_Immune_Diversity_Atlas": 0.09557,
+   "007_A_collection_e1a9ca56-f2ee-435d-980a-4f49ab7a95_Miao_et_al._RA_PBMC_disease_activity-associated_PBMC_subsets": 0.00554,
+   "009_A_Human_Immune_Health_Atlas_Human_Immune_Health_Atlas_AIFI_immune_dynamics_across_healthy_age": 0.01644,
+   "010_A_collection_4a9fd4d7-d870-4265-89a5-ad51ab811d_ScaleBio_single-cell_RNA_sequencing_of_human_PBMCs": 0.00019,
+   "053_B_collection_b0cf0afa-ec40-4d65-b570-ed4ceacc68_Integrated_analysis_of_multimodal_single-cell_data_CITE-seq_PBMC": 0.00344,
+   "058_B_collection_eb735cc9-d0a7-48fa-b255-db726bf365_COVID_PBMC_nasal_swab_donors_with_immunodeficiencies_and_autoimmune_conditions": 0.00344,
+   "061_A_GSE274680_Savage_Allen_RA_at-risk_longitudinal_progression_PBMC_multi-omic_cohort": 0.03651,
+   "065_A_GSE271896_GSE271896_Sound_Life_deep_longitudinal_immune_profiling": 0.1336,
+   "071_C_JDM_CITE-seq_PBMC_CELLxGENE_JDM_CITE-seq_PBMC_CELLxGENE": 0.01644,
+   "074_A_COMBAT_CELLxGENE_collection_COMBAT_CELLxGENE_collection": 0.02179,
+   "081_B_Single-cell_atlas_of_peripheral_immune_respon_Single-cell_atlas_of_peripheral_immune_response_to_SARS-CoV-2": 0.0021,
+   "093_C_Local_and_systemic_SARS-CoV-2_response_CELLxG_Local_and_systemic_SARS-CoV-2_response_CELLxGENE": 0.01223,
+   "200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling": 0.03574,
+   "202_B_GSE161918_Time-resolved_Systems_Immunology_Reveals_a_Late_Juncture_Linked_to_Fatal_COVID-1": 0.01414,
+   "203_B_CELLxGENE_665714af_Ancestral_and_environmental_diversity_shape_the_immune_landscape_in_Indonesia": 0.03039,
+   "204_B_CELLxGENE_cHSPC_aging_MDS_Human_circulating_hematopoietic_stem_and_progenitor_cells_in_aging_cytopenia_and": 0.0367,
+   "300b_A_GSE132802_DRESS_DiHS_PBMC_only_scRNAseq": 0.00096,
+   "301_A_GSE163121_SLE_healthy_Bcell_PBMC_scRNAseq": 0.00057,
+   "302_A_GSE314010_SLE_IL36_stim_PBMC_scRNAseq": 0.00057,
+   "304_A_Parse_10M_PBMC_12donor_90cytokines": 0.17393
+  }
+ },
+ "variant_agreement_vs_primary": {
+  "recipes_all_epochs": {
+   "pearson_log1p_mean_cpm_all_present": 0.999981753857617,
+   "pearson_log1p_mean_cpm_model_genes": 0.9999680869009335,
+   "mean_abs_log1p_diff_all_present": 0.00872456116021775
+  },
+  "cells_all_epochs": {
+   "pearson_log1p_mean_cpm_all_present": 0.999977932571947,
+   "pearson_log1p_mean_cpm_model_genes": 0.9999632108182864,
+   "mean_abs_log1p_diff_all_present": 0.006911143294236873
+  },
+  "samples_equal": {
+   "pearson_log1p_mean_cpm_all_present": 0.9901830694298792,
+   "pearson_log1p_mean_cpm_model_genes": 0.9853761815578563,
+   "mean_abs_log1p_diff_all_present": 0.2398217409504203
+  }
+ },
+ "measurement": {
+  "n_present_primary": 20024,
+  "n_present_full_weight_primary": 13115,
+  "n_present_partial_weight_primary": 6909,
+  "n_present_below_half_weight_primary": 429,
+  "model_genes_partial_weight_primary": 1212,
+  "model_genes_below_half_weight_primary": 73,
+  "model_genes_not_present": 0,
+  "samples_with_mask_mixed_across_shards": 2146,
+  "counts_on_coordinates_dropped_by_and_mask": 143120.0
+ },
+ "composition_celltype_l1_weighted_primary": {
+  "B cell": 0.10673783592523547,
+  "DC": 0.01117509691127314,
+  "Erythrocyte": 0.0011723390470993,
+  "Granulocyte": 0.000330922378775805,
+  "ILC": 0.0005990158857269874,
+  "Mast cell": 3.367543586113128e-06,
+  "Monocyte": 0.1958524225343244,
+  "NK cell": 0.07804016934083413,
+  "NKT cell": 0.0002664738937711722,
+  "Neutrophil": 0.00020489624276325875,
+  "Platelet": 0.002722994773664946,
+  "Progenitor cell": 0.035325784966429755,
+  "T cell": 0.5573650202224748,
+  "__unknown__": 0.006079858841090219,
+  "unlabelled": 0.004123801492950508
+ },
+ "monocyte_fraction_per_sample_primary_weighted_median": 0.18175937904269082,
+ "output": {
+  "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/refcal_refs/reference/train_distribution_reference_20097.npz",
+  "sha256": "e9036c7b5661d986581a4eb60fdedc2df8a1cdb3bcf1941e4418df6bb951b063",
+  "bytes": 4022460
+ },
+ "elapsed_s": 274.4
+}

paper-releases/20260928/diffusion/data/calibration/train_distribution_reference_20097.npz ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:e9036c7b5661d986581a4eb60fdedc2df8a1cdb3bcf1941e4418df6bb951b063
+size 4022460

paper-releases/20260928/diffusion/data/cohorts/giroux2022/MANIFEST.json ADDED Viewed

	@@ -0,0 +1,749 @@

+{
+ "schema": "giroux2022_paired_ft_v1",
+ "written_utc": "2026-09-28T02:58:52.766313+00:00",
+ "started_utc": "2026-09-28T02:58:13.308829+00:00",
+ "study": "Giroux NS et al., Sci Rep 2022 (doi 10.1038/s41598-022-15668-8; PMID 35810186); SuperSeries GSE206284; bulk GSE206263, scRNA GSE206283",
+ "rows": 26,
+ "subjects": 10,
+ "row_order": "bulk GSM ascending (subject blocks, day ascending)",
+ "pairs_by_group": {
+  "mild": 13,
+  "severe": 13
+ },
+ "pairs_by_timepoint": {
+  "0": 10,
+  "14": 9,
+  "7": 7
+ },
+ "pairs_by_subject": {
+  "0B943B": "0,14",
+  "0BF51C": "0,7,14",
+  "180E1A": "0,7,14",
+  "2AD75E": "0,7,14",
+  "40067F": "0,14",
+  "450905": "0,14",
+  "7085CA": "0,7,14",
+  "82CCF5": "0,7,14",
+  "B85D75": "0,7",
+  "BAAF62": "0,7,14"
+ },
+ "pairs_by_id_match": {
+  "exact_subject_day": 26
+ },
+ "cells": {
+  "n_cells": 276615,
+  "nnz": 98611153,
+  "per_row_min": 5914,
+  "per_row_median": 10958.0,
+  "per_row_max": 15650
+ },
+ "retained_cells_rule": "flag_conservative_review_pass = genes>=200 & UMIs>=500 & mito<=20% (qc_core, ImMicro definition); MAD flags are review-only columns",
+ "features_semantics": {
+  "bulk_raw": "author featureCounts raw gene counts (STAR/hg19) mapped by gene symbol to the canonical axis; 0 where bulk_valid is False (ImMicro file uses NaN there); 3 many-to-one symbol groups summed (bundle policy for verified integer counts)",
+  "pseudo_raw_sum": "sum of retained cells' UMI counts on the canonical axis; storage 0 where sc_valid is False",
+  "bulk_valid": "harmonization_valid from qc_bulk.harmonize (symbol in the author table maps uniquely to the canonical gene)",
+  "sc_valid": "harmonization_valid from qc_singlecell.canonical_export (gene in the 10x features table)",
+  "pair_valid": "bulk_valid & sc_valid",
+  "sample_ids": "<subject>_d<day>, e.g. 450905_d0",
+  "donor_ids": "GEO subject ID (6-hex); a subject has 2-3 rows (days)",
+  "timepoints": "GEO sampling day (int64: 0, 7 or 14 among pairs)",
+  "groups": "GEO 'exposure' field lower-cased: mild, severe (the paper and the author sample sheet call this group 'moderate'; kept in author_cohort), exposed, healthy; only mild and severe have pairs",
+  "extra_keys": "bulk_gsm, sc_gsm, sc_title_sample_id (GEO sc title), id_match, bulk_count_column (author table column), sc_author_library (author library name), sex_geo, age_geo, serostatus_geo (IgG), author_cohort, identity_pass, identity_check, sex_bulk_expr, sex_sc_expr",
+  "not_applicable": "Ye 2026 keys infection_source and collection_site have no counterpart here"
+ },
+ "identity": {
+  "sex_rule": "CPM on the source axis (bulk: all 26,045 author-table genes; sc: retained cells, all RNA features); score=log2(XIST+1)-log2(Ysum+1); female>2, male<-2, else ambiguous. Bulk Ysum = DDX3Y+UTY+KDM5D (RPS4Y1 is not in the author table); sc Ysum = RPS4Y1+DDX3Y+UTY+KDM5D (3-gene sc call also reported); opposite-sex signal flag: female call with Y CPM>20 or male call with XIST CPM>50 (bulk)",
+  "expression_rule": "log2(CPM+1) over the 18240 non-chrY canonical genes measured in all 49 bulk columns and all 41 sc libraries; top 2000 by the mean of the bulk-mean and sc-mean log CPM; Spearman of each paired bulk vs all sc pseudobulks; centred sensitivity; reverse vs all 49 bulks",
+  "expression_residualised_rule": "within each modality: centre log2(CPM+1) (same genes), remove the top k sample PCs computed on expressed genes (bulk mean >3 and sc mean >1 log2 CPM), keep the 2000 genes with the highest residual variance in both modalities (rank sum), Pearson over all 49 bulks x all 41 sc libraries. k=5 primary (41 sc libraries and 49 bulks, vs 133/207 with k=10 for Ye 2026), k=3 and k=10 sensitivity. Ranks are reported per library and per subject (each subject scored by its best sample). chrY genes are excluded so the test is independent of the sex check. Uses no pairing information.",
+  "verdict_rule": "pass = sex concordant (bulk, sc, GEO) and residualised k=5 own subject ranked 1st in one direction and within the top 3 subjects in the other and no day failure; fail = sex discordant, or own subject below 3 in both directions, or day failure; else borderline",
+  "day_check": "within the subject's paired rows, rank of the own day on the residualised (k=5) and on the centred (not residualised; top 2000 genes by centred variance in both modalities) expression correlation, both directions. Day failure = another day of the same subject beats the own day in all four. Added after the subject-level test was seen to be blind to within-subject day swaps (the task requires the same sampling day).",
+  "isg_rule": "informational: mean log2(CPM+1) of 12 ISGs (IFI27, IFI44L, ISG15, RSAD2, IFIT1, IFIT3, MX1, OAS1, OAS3, SIGLEC1, IFI6, HERC5) per sample; per subject the ISG-peak day in bulk and in sc is reported",
+  "policy": "reported only; no row dropped on identity results; features.npz carries identity_pass / identity_check"
+ },
+ "checks": {
+  "gene_positions_sha256_ok": true,
+  "panel_gene_ids_match_selected_genes_csv": true,
+  "bulk_integer_nonnegative_inside_mask": true,
+  "pseudo_raw_sum_equals_sum_of_retained_cells_full_axis": true,
+  "cells_panel_sums_equal_pseudo_raw_sum_positions_exactly": true,
+  "cells_per_row_equal_qc_cell_counts": true,
+  "no_sc_mass_outside_sc_valid": true,
+  "one_sample_id_per_library": true,
+  "bulk_and_sc_GSM_agree_on_age_sex_group_serostatus": true,
+  "sex_concordant_pairs": "26/26",
+  "sc_sex_call_4gene_equals_3gene_all_41_libraries": true,
+  "expression_best_match_is_own_pair": "4/26",
+  "expression_best_match_is_own_pair_centred": "12/26",
+  "expression_reverse_best_match_is_own_pair": "3/26",
+  "expression_residualised_k5_own_subject_top1_bulk_to_sc": "26/26",
+  "expression_residualised_k3_own_subject_top1_bulk_to_sc": "26/26",
+  "expression_residualised_k10_own_subject_top1_bulk_to_sc": "24/26",
+  "expression_residualised_k5_own_subject_top1_sc_to_bulk": "26/26",
+  "expression_residualised_k3_own_subject_top1_sc_to_bulk": "25/26",
+  "expression_residualised_k10_own_subject_top1_sc_to_bulk": "20/26",
+  "expression_residualised_k5_own_library_top1_bulk_to_sc": "23/26",
+  "expression_residualised_k3_own_library_top1_bulk_to_sc": "24/26",
+  "expression_residualised_k10_own_library_top1_bulk_to_sc": "22/26",
+  "expression_residualised_k5_own_day_best_within_subject_bulk_to_sc": "24/26",
+  "expression_residualised_k5_own_day_best_within_subject_sc_to_bulk": "22/26",
+  "expression_centred_own_day_best_within_subject_bulk_to_sc": "20/26",
+  "expression_centred_own_day_best_within_subject_sc_to_bulk": "21/26",
+  "isg_peak_day_same_in_both_assays_subjects": "9/10",
+  "identity_check_pass": "24/26",
+  "identity_check_fail": [
+   "40067F_d0",
+   "40067F_d14"
+  ],
+  "identity_check_borderline": []
+ },
+ "excluded": {
+  "quarantined_sc_libraries_among_pairs": [],
+  "sc_libraries_without_pair": [
+   {
+    "sc_gsm": "GSM6249237",
+    "sample_id": "450905_d7",
+    "group": "mild",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249239",
+    "sample_id": "7768E4_d2",
+    "group": "exposed",
+    "pair_status": "no_bulk_GSM_for_this_subject_day"
+   },
+   {
+    "sc_gsm": "GSM6249240",
+    "sample_id": "7768E4_d14",
+    "group": "exposed",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249241",
+    "sample_id": "7768E4_d28",
+    "group": "exposed",
+    "pair_status": "no_bulk_GSM_for_this_subject_day"
+   },
+   {
+    "sc_gsm": "GSM6249243",
+    "sample_id": "0B943B_d3",
+    "group": "mild",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249262",
+    "sample_id": "61BBAD_d0",
+    "group": "exposed",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249263",
+    "sample_id": "61BBAD_d7",
+    "group": "exposed",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249264",
+    "sample_id": "61BBAD_d14",
+    "group": "exposed",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249267",
+    "sample_id": "80A16A_d0",
+    "group": "exposed",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249268",
+    "sample_id": "80A16A_d14",
+    "group": "exposed",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249272",
+    "sample_id": "E0FA1E_dNA",
+    "group": "healthy",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249273",
+    "sample_id": "3F3322_dNA",
+    "group": "healthy",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249274",
+    "sample_id": "94D44E_dNA",
+    "group": "healthy",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249275",
+    "sample_id": "52BA23_dNA",
+    "group": "healthy",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   },
+   {
+    "sc_gsm": "GSM6249276",
+    "sample_id": "655A91_dNA",
+    "group": "healthy",
+    "pair_status": "bulk_GSM_has_no_column_in_author_count_table"
+   }
+  ],
+  "bulk_count_columns_without_pair": [
+   {
+    "bulk_column": "062CD8",
+    "bulk_gsm": "GSM6248878",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "77DA77",
+    "bulk_gsm": "",
+    "unpaired_reason": "column_name_not_a_GEO_subject_day"
+   },
+   {
+    "bulk_column": "22CBD6",
+    "bulk_gsm": "",
+    "unpaired_reason": "column_name_not_a_GEO_subject_day"
+   },
+   {
+    "bulk_column": "4F2EAD",
+    "bulk_gsm": "",
+    "unpaired_reason": "column_name_not_a_GEO_subject_day"
+   },
+   {
+    "bulk_column": "F8FF1A",
+    "bulk_gsm": "",
+    "unpaired_reason": "column_name_not_a_GEO_subject_day"
+   },
+   {
+    "bulk_column": "56E219",
+    "bulk_gsm": "",
+    "unpaired_reason": "column_name_not_a_GEO_subject_day"
+   },
+   {
+    "bulk_column": "40067F-21",
+    "bulk_gsm": "GSM6248857",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "E9CFE0",
+    "bulk_gsm": "GSM6248882",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "1A9B20-0",
+    "bulk_gsm": "GSM6248837",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "1A9B20-14",
+    "bulk_gsm": "GSM6248839",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "1A9B20-7",
+    "bulk_gsm": "GSM6248838",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "75A2B6-0",
+    "bulk_gsm": "GSM6248843",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "75A2B6-14",
+    "bulk_gsm": "GSM6248845",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "75A2B6-7",
+    "bulk_gsm": "GSM6248844",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "DF309F-0",
+    "bulk_gsm": "GSM6248846",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "DF309F-14",
+    "bulk_gsm": "GSM6248848",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "DF309F-7",
+    "bulk_gsm": "GSM6248847",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "3F05F3-0",
+    "bulk_gsm": "GSM6248849",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "3F05F3-14",
+    "bulk_gsm": "",
+    "unpaired_reason": "column_name_not_a_GEO_subject_day"
+   },
+   {
+    "bulk_column": "3F05F3-7",
+    "bulk_gsm": "GSM6248850",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "0E1F8E-0",
+    "bulk_gsm": "GSM6248858",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "0E1F8E-14",
+    "bulk_gsm": "GSM6248860",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   },
+   {
+    "bulk_column": "0E1F8E-7",
+    "bulk_gsm": "GSM6248859",
+    "unpaired_reason": "no_sc_library_for_this_subject_day"
+   }
+  ],
+  "bulk_GSMs_without_author_count_column": [
+   {
+    "gsm": "GSM6248815",
+    "sample_id": "450905_d7",
+    "group": "mild"
+   },
+   {
+    "gsm": "GSM6248817",
+    "sample_id": "7768E4_d0",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248818",
+    "sample_id": "7768E4_d7",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248819",
+    "sample_id": "7768E4_d14",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248821",
+    "sample_id": "0B943B_d3",
+    "group": "mild"
+   },
+   {
+    "gsm": "GSM6248851",
+    "sample_id": "3F05F3_d28",
+    "group": "severe"
+   },
+   {
+    "gsm": "GSM6248852",
+    "sample_id": "61BBAD_d0",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248853",
+    "sample_id": "61BBAD_d7",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248854",
+    "sample_id": "61BBAD_d14",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248861",
+    "sample_id": "CE0CE8_d0",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248862",
+    "sample_id": "CE0CE8_d14",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248863",
+    "sample_id": "CE0CE8_d28",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248864",
+    "sample_id": "80A16A_d0",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248865",
+    "sample_id": "80A16A_d14",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248869",
+    "sample_id": "5ABDCB_d0",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248870",
+    "sample_id": "5ABDCB_d14",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248871",
+    "sample_id": "5ABDCB_d28",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248872",
+    "sample_id": "B96D3B_d0",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248873",
+    "sample_id": "B96D3B_d14",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248874",
+    "sample_id": "B96D3B_d28",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248875",
+    "sample_id": "6F894A_d0",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248876",
+    "sample_id": "6F894A_d7",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248877",
+    "sample_id": "6F894A_d14",
+    "group": "exposed"
+   },
+   {
+    "gsm": "GSM6248879",
+    "sample_id": "E0FA1E_dNA",
+    "group": "healthy"
+   },
+   {
+    "gsm": "GSM6248880",
+    "sample_id": "3F3322_dNA",
+    "group": "healthy"
+   },
+   {
+    "gsm": "GSM6248881",
+    "sample_id": "94D44E_dNA",
+    "group": "healthy"
+   },
+   {
+    "gsm": "GSM6248883",
+    "sample_id": "52BA23_dNA",
+    "group": "healthy"
+   },
+   {
+    "gsm": "GSM6248884",
+    "sample_id": "655A91_dNA",
+    "group": "healthy"
+   }
+  ]
+ },
+ "leads_not_pairs": {
+  "note": "unpaired author bulk columns that have no GEO GSM vs all sc libraries (residualised k=5); a lead is NOT a pair: no published ID links these columns to GEO subjects",
+  "rows": [
+   {
+    "bulk_column": "77DA77",
+    "bulk_sex_call": "female",
+    "best_sc_gsm": "GSM6249272",
+    "best_sc_sample": "E0FA1E_dNA",
+    "best_sc_sex_call": "female",
+    "best_sc_geo_sex": "FEMALE",
+    "best_sc_is_unpaired": true,
+    "r_best": 0.420464334761289,
+    "r_second": 0.24960839890653738,
+    "second_sc_sample": "180E1A_d0",
+    "reverse_rank_of_this_bulk_for_best_sc": 1,
+    "reverse_best_bulk_for_best_sc": "77DA77",
+    "geo_healthy_subject_at_same_position_in_author_sheet": "E0FA1E",
+    "position_agrees_with_best_sc_subject": true
+   },
+   {
+    "bulk_column": "22CBD6",
+    "bulk_sex_call": "female",
+    "best_sc_gsm": "GSM6249273",
+    "best_sc_sample": "3F3322_dNA",
+    "best_sc_sex_call": "female",
+    "best_sc_geo_sex": "FEMALE",
+    "best_sc_is_unpaired": true,
+    "r_best": 0.5237721652596927,
+    "r_second": 0.23295362914335938,
+    "second_sc_sample": "2AD75E_d14",
+    "reverse_rank_of_this_bulk_for_best_sc": 1,
+    "reverse_best_bulk_for_best_sc": "22CBD6",
+    "geo_healthy_subject_at_same_position_in_author_sheet": "3F3322",
+    "position_agrees_with_best_sc_subject": true
+   },
+   {
+    "bulk_column": "4F2EAD",
+    "bulk_sex_call": "female",
+    "best_sc_gsm": "GSM6249274",
+    "best_sc_sample": "94D44E_dNA",
+    "best_sc_sex_call": "female",
+    "best_sc_geo_sex": "FEMALE",
+    "best_sc_is_unpaired": true,
+    "r_best": 0.5762409562275047,
+    "r_second": 0.2055064434130179,
+    "second_sc_sample": "450905_d0",
+    "reverse_rank_of_this_bulk_for_best_sc": 1,
+    "reverse_best_bulk_for_best_sc": "4F2EAD",
+    "geo_healthy_subject_at_same_position_in_author_sheet": "94D44E",
+    "position_agrees_with_best_sc_subject": true
+   },
+   {
+    "bulk_column": "F8FF1A",
+    "bulk_sex_call": "male",
+    "best_sc_gsm": "GSM6249275",
+    "best_sc_sample": "52BA23_dNA",
+    "best_sc_sex_call": "male",
+    "best_sc_geo_sex": "MALE",
+    "best_sc_is_unpaired": true,
+    "r_best": 0.6572060268667277,
+    "r_second": 0.2232559108831267,
+    "second_sc_sample": "61BBAD_d14",
+    "reverse_rank_of_this_bulk_for_best_sc": 1,
+    "reverse_best_bulk_for_best_sc": "F8FF1A",
+    "geo_healthy_subject_at_same_position_in_author_sheet": "52BA23",
+    "position_agrees_with_best_sc_subject": true
+   },
+   {
+    "bulk_column": "56E219",
+    "bulk_sex_call": "female",
+    "best_sc_gsm": "GSM6249276",
+    "best_sc_sample": "655A91_dNA",
+    "best_sc_sex_call": "female",
+    "best_sc_geo_sex": "FEMALE",
+    "best_sc_is_unpaired": true,
+    "r_best": 0.709301480946846,
+    "r_second": 0.3301510549216415,
+    "second_sc_sample": "80A16A_d0",
+    "reverse_rank_of_this_bulk_for_best_sc": 1,
+    "reverse_best_bulk_for_best_sc": "56E219",
+    "geo_healthy_subject_at_same_position_in_author_sheet": "655A91",
+    "position_agrees_with_best_sc_subject": true
+   },
+   {
+    "bulk_column": "3F05F3-14",
+    "bulk_sex_call": "male",
+    "best_sc_gsm": "GSM6249243",
+    "best_sc_sample": "0B943B_d3",
+    "best_sc_sex_call": "male",
+    "best_sc_geo_sex": "MALE",
+    "best_sc_is_unpaired": true,
+    "r_best": 0.21044879494769114,
+    "r_second": 0.1687903603213745,
+    "second_sc_sample": "82CCF5_d0",
+    "reverse_rank_of_this_bulk_for_best_sc": 5,
+    "reverse_best_bulk_for_best_sc": "2AD75E-7",
+    "geo_healthy_subject_at_same_position_in_author_sheet": "",
+    "position_agrees_with_best_sc_subject": false
+   }
+  ]
+ },
+ "inputs": {
+  "gene_positions": {
+   "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/6k/gene_positions.npy",
+   "sha256": "653ffa45ac519000baa41086c52408009391d6e68cfb218bc6a50d34163fcb24"
+  },
+  "selected_genes": {
+   "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/6k/selected_genes.csv",
+   "sha256": "09248a3930e3fdefe1dbcd5d60cae4be81028526dcf097dd78169f5a415edfb6"
+  },
+  "canonical_genes": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/reference/canonical_genes.tsv",
+   "sha256": "484893b6f6ab673566074e0d2f32c4ec6628ced63f7e709b38ec602cb3e776ab"
+  },
+  "bulk_harmonized": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/bulk/GSE206263_featureCounts/harmonized.h5ad",
+   "sha256": "7c8a591deec997ed731ee56638e83d929b67d81cbdbbad9406259f355e1d0ffb"
+  },
+  "sources": [
+   {
+    "accession": "GSE206263",
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/GSE206263/metadata/GSE206263_family.soft.gz",
+    "bytes": 6016,
+    "sha256": "5b3a177a534bfa9c632a33056557aa43cb95b74e3557b3817f6e66a2b3da0f31",
+    "acquisition_receipt": true,
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206263/soft/GSE206263_family.soft.gz",
+    "receipt_sha256": "5b3a177a534bfa9c632a33056557aa43cb95b74e3557b3817f6e66a2b3da0f31",
+    "receipt_bytes": 6016,
+    "receipt_completed_at": "2026-09-27T04:45:33.765586+00:00",
+    "matches_receipt": true
+   },
+   {
+    "accession": "GSE206263",
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/GSE206263/raw/GSE206263_bulkRNA_processed.tar.gz",
+    "bytes": 1577319,
+    "sha256": "0cf488dbd0667a0ee04fff8a8ee44350cdb68f1325b25eab06441057235728a7",
+    "acquisition_receipt": true,
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206263/suppl/GSE206263_bulkRNA_processed.tar.gz",
+    "receipt_sha256": "0cf488dbd0667a0ee04fff8a8ee44350cdb68f1325b25eab06441057235728a7",
+    "receipt_bytes": 1577319,
+    "receipt_completed_at": "2026-09-27T04:45:45.882668+00:00",
+    "matches_receipt": true
+   },
+   {
+    "accession": "GSE206283",
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/GSE206283/metadata/GSE206283_family.soft.gz",
+    "bytes": 5640,
+    "sha256": "d13ffbfd655c7dad5e236889ec89fab4f7ef048a24edac4db1765a1106e76d56",
+    "acquisition_receipt": true,
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206283/soft/GSE206283_family.soft.gz",
+    "receipt_sha256": "d13ffbfd655c7dad5e236889ec89fab4f7ef048a24edac4db1765a1106e76d56",
+    "receipt_bytes": 5640,
+    "receipt_completed_at": "2026-09-27T04:45:32.408263+00:00",
+    "matches_receipt": true
+   },
+   {
+    "accession": "GSE206283",
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/GSE206283/raw/GSE206283_RAW.tar",
+    "bytes": 2326763520,
+    "sha256": "17599bb1fca707204353c69b07c1f90a7784aa9664a419dbe99416df789b0729",
+    "acquisition_receipt": true,
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206283/suppl/GSE206283_RAW.tar",
+    "receipt_sha256": "17599bb1fca707204353c69b07c1f90a7784aa9664a419dbe99416df789b0729",
+    "receipt_bytes": 2326763520,
+    "receipt_completed_at": "2026-09-27T04:57:52.246904+00:00",
+    "matches_receipt": true
+   }
+  ],
+  "external_metadata": [
+   {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/external_metadata/GSE206263_series_matrix.txt.gz",
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206263/matrix/GSE206263_series_matrix.txt.gz",
+    "bytes": 5032,
+    "sha256": "ea359a691cebddaa3feefc41f86f68c41acf227c89d5b9fdbff9370072138108"
+   },
+   {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/external_metadata/GSE206266_family.soft.gz",
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206266/soft/GSE206266_family.soft.gz",
+    "bytes": 6614,
+    "sha256": "950347645a631858729099a02eb3e463f5da94bec1a6b27ff6c3455f4c835bdf"
+   },
+   {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/external_metadata/GSE206283_series_matrix.txt.gz",
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206283/matrix/GSE206283_series_matrix.txt.gz",
+    "bytes": 5044,
+    "sha256": "6a3937711a3fe60e8d8f62166657b077e2d85bad59b15bf7b7b3d1ea640b9c38"
+   },
+   {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/external_metadata/GSE206284_family.soft.gz",
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206284/soft/GSE206284_family.soft.gz",
+    "bytes": 16100,
+    "sha256": "1fdf1c7578ebea33d3b0ad29663d31365b55c18c34676b72fd42fada75036911"
+   },
+   {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/external_metadata/GSE206455_family.soft.gz",
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206455/soft/GSE206455_family.soft.gz",
+    "bytes": 5586,
+    "sha256": "397beca3d72f2da2ef0adc8d875095502c4d3aa5b4c0f50cb261bc03604a1880"
+   },
+   {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/external_metadata/biosample_healthy.xml",
+    "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample&id=SAMN29146766,SAMN29146767,SAMN29146831&retmode=xml",
+    "bytes": 7599,
+    "sha256": "8cb48e0a6b0d35f6dc6d0c379648c89ef2746c6ec908d6faca6eeebd521fe5fa"
+   },
+   {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/external_metadata/geo_download_page_GSE206263.html",
+    "url": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE206263 (no NCBI-generated RNA-seq count file offered; type=rnaseq_counts URL returns 404)",
+    "bytes": 6524,
+    "sha256": "f50b30ca002b72e4d8c921c75b6bf3dc5709c7160071faefb12663722f775156"
+   },
+   {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/external_metadata/sra_runinfo_bulk.csv",
+    "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&term=PRJNA849921&rettype=runinfo (via esearch history)",
+    "bytes": 49831,
+    "sha256": "9e4f5558a0c2e893966ac8a328ed6f1ec72ddc64a9af6cf6212ad40a33a4f0cd"
+   }
+  ]
+ },
+ "code": {
+  "assemble": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/giroux2022_assemble.py",
+   "sha256": "68fff8c927403034122b0ba26e1cd112a75d280a094de5939375059dd2146d65"
+  },
+  "pipeline": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/giroux2022_pipeline.py",
+   "sha256": "115dc5397554ec4a7c8efa05e30f7d7beef9b456a02785a4fd8d8615620c4e19"
+  },
+  "run_step": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/run_step.sh",
+   "sha256": "1c889d55dee20bd8fd0d4e0696cf1ec1f48dbf4a40affc916fea81a690a885c4"
+  },
+  "bundle/qc_bulk.py": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/strict_qc_v1_code_bundle_v5/qc_bulk.py",
+   "sha256": "8c3bd5179a11c25fdeea491d7071bd492faaabc3cff3348a0750de199cddae9c"
+  },
+  "bundle/qc_core.py": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/strict_qc_v1_code_bundle_v5/qc_core.py",
+   "sha256": "b50a175b64044142676c8c55f9630da90d8c0c193c761124de9ef02d517e4851"
+  },
+  "bundle/qc_finalize.py": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/strict_qc_v1_code_bundle_v5/qc_finalize.py",
+   "sha256": "c4acc068779e3823869bafa4cb8a9384b60b3e66693bbacc313758d0bd495f0a"
+  },
+  "bundle/qc_genes.py": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/strict_qc_v1_code_bundle_v5/qc_genes.py",
+   "sha256": "ff93bbc364af6a0822b0cff7c5ef0fb407aa2512bc8afa6f0681754f0fb65c86"
+  },
+  "bundle/qc_singlecell.py": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/strict_qc_v1_code_bundle_v5/qc_singlecell.py",
+   "sha256": "a69ab1e0b1686e466474735b67a398f5d2140936e66a95051d02a6a497a59753"
+  },
+  "bundle/qc_validate_outputs.py": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/strict_qc_v1_code_bundle_v5/qc_validate_outputs.py",
+   "sha256": "8fe39a62b38f40e3e6053e9300abe81818a27f0e39a044e660eb88c094480daa"
+  },
+  "bundle/strict_qc_driver.py": {
+   "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/code/strict_qc_v1_code_bundle_v5/strict_qc_driver.py",
+   "sha256": "88ec34fb10074334a4e4ba2f4059a9b04ade1ba3b335d2c448a1f67594daa078"
+  }
+ },
+ "processing_dir": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928",
+ "outputs": {
+  "cells_obs.parquet": {
+   "bytes": 7303369,
+   "sha256": "e2d1c0c490563d0e9858c6e8d3680d702ce14a180ce75101e305e95be572e618"
+  },
+  "cells_panel6k.npz": {
+   "bytes": 186701727,
+   "sha256": "7d22c0ff4b3af2b1fd1741421633616b5ab0e679a800ecffb780cc5fd1b507d1"
+  },
+  "features.npz": {
+   "bytes": 2111068,
+   "sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5"
+  },
+  "identity_expression.csv": {
+   "bytes": 13655,
+   "sha256": "4aa3ad85547f3eba9be9c9b8afecc52a90382be9936bae33c6b8be9c409aea3e"
+  },
+  "identity_sex_bulk_all.csv": {
+   "bytes": 7588,
+   "sha256": "af2f8065b999ade06f724e9011d027bac65ea36231d3e48f86db018c376aa37c"
+  },
+  "identity_sex_sc_all.csv": {
+   "bytes": 8312,
+   "sha256": "a6b3628b100d2f9734697248ff3381c4a7d63dd768ffb967ad70c6789e2edaa8"
+  },
+  "pairs.csv": {
+   "bytes": 22584,
+   "sha256": "f590c76cbf02ad8ddfa7173bc668cb8c75a9e4c0bf2c6e50b211960dd9523b27"
+  },
+  "samples.csv": {
+   "bytes": 860,
+   "sha256": "591b4b697bdf405da35a35ece829db282bb59c70317160711500dda1ed1a5f5c"
+  }
+ }
+}

paper-releases/20260928/diffusion/data/cohorts/giroux2022/PREPARE.json ADDED Viewed

	@@ -0,0 +1,90 @@

+{
+ "schema": "pbisc_sdd.ft_intradataset.conditions.v1",
+ "dataset": "giroux2022",
+ "written_utc": "2026-09-28T03:00:47.485835+00:00",
+ "features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
+ "seed": 20260927,
+ "folds": 5,
+ "inner_frac": 0.1,
+ "cells_per_bulk": 1500,
+ "recipe_k": 1000,
+ "depth_anchor": 3869.603120208939,
+ "builder": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/realbulk_generation_20260922/build_realbulk_conditions.py",
+ "builder_sha256": "e818d69e6801b5699579db7fc450590a266708d1fc2d544743e8624c9ee6a30a",
+ "files": {
+  "conditions_raw_fixed.npz": "b584655fcfa5fa4c0887d5dd83fcb1c5a0206da4afe5fefab96cba2272b1371c",
+  "conditions_pseudo_fixed.npz": "24283f6bbc7dc0caf281e1a0f7ba2e843504d941f6860c453186a163b4476303",
+  "fold0/conditions_cal_fixed.npz": "eedf86d9be962b6adcd4590c15fffd332d6c6f0c0abb0f09ef66de4425fd8e5f",
+  "fold0/test_raw.npz": "f4c4b313f3f5524b298ddf8bbda38623a4db03946c2003998f52aa114d69fa7f",
+  "fold0/test_cal.npz": "4f5cdfc0d93a4f3ef2974fea79506bd1c3f8305f74d41a3539397b17fdc96e4f",
+  "fold0/test_pseudo.npz": "a76a46830da686398fb4b43f841a2158943b20436d3e063a295a043b17f6a461",
+  "fold1/conditions_cal_fixed.npz": "94c91e1a702ba419edf28a810a9c2ac73e39dc21af18c70d245400177a6c8001",
+  "fold1/test_raw.npz": "8bf4424b2aa1eada997a9c82f320efa6498530fdabd95e330555c0bd201a5d51",
+  "fold1/test_cal.npz": "ceeb27ce0dfb141b40938e8096b7bb4c56a018a74ac4850b11eb7d24d5e46279",
+  "fold1/test_pseudo.npz": "020f23cd44334332564bc79eaf5851638a7832a5d0209925be12f656570ce9cd",
+  "fold2/conditions_cal_fixed.npz": "496eb078719dc4d3af2b6de6f8722d138c63bf11e0ac19db8e2c4a00c7a14186",
+  "fold2/test_raw.npz": "90810fa9b6fef46663327f6486e61d7aafeacd5fc0c95513e6fdd7f46023bcb5",
+  "fold2/test_cal.npz": "452d8012fe3f254de249f4f73882e962b13ec9774e5f69370d5315c5d0dac20a",
+  "fold2/test_pseudo.npz": "a76a4d4e6932dc1154d11d6f7d1add2deee514707e6e4449daa12d57397f4ff6",
+  "fold3/conditions_cal_fixed.npz": "719d1a1870a9123bdfb35ffeb13ed892976215e67bf866a6cba2282b41e0c087",
+  "fold3/test_raw.npz": "f520b7350ba8102fc1bceccc2db1b1a993f082ad62ec4b68dd3eef28c1162dc3",
+  "fold3/test_cal.npz": "8967f1ad858f51f73b1e3ea00e25c0395b733916f61bb892c1690d9f34ceb4c6",
+  "fold3/test_pseudo.npz": "a740e8bb76ea44eea02eba41bbc247ef1d65ea0a4e012589415b7785fc93a2a5",
+  "fold4/conditions_cal_fixed.npz": "17bbe9d8328e0ce5a54fd1ec438891f2dbfb18e29c220bc69e322ffcfe8be66a",
+  "fold4/test_raw.npz": "a91f8fb3638328147b86f2f2728954c3257aa63e73429cf04d4741a75e11aa60",
+  "fold4/test_cal.npz": "d8af1fb9d3111284a083c77cc88f157d1e09619384b16e2445e9ebb461732599",
+  "fold4/test_pseudo.npz": "6706804bc04aa255e591d18074aeb835967e335de6dd8458833e1b722a376a39"
+ },
+ "fold_sizes": {
+  "0": {
+   "test": 4,
+   "train": 18,
+   "inner_val": 2,
+   "test_groups": {
+    "mild": 2,
+    "severe": 2
+   },
+   "alpha_genes_estimated": 10803
+  },
+  "1": {
+   "test": 5,
+   "train": 16,
+   "inner_val": 3,
+   "test_groups": {
+    "severe": 3,
+    "mild": 2
+   },
+   "alpha_genes_estimated": 10794
+  },
+  "2": {
+   "test": 6,
+   "train": 15,
+   "inner_val": 3,
+   "test_groups": {
+    "mild": 3,
+    "severe": 3
+   },
+   "alpha_genes_estimated": 10839
+  },
+  "3": {
+   "test": 6,
+   "train": 16,
+   "inner_val": 2,
+   "test_groups": {
+    "severe": 3,
+    "mild": 3
+   },
+   "alpha_genes_estimated": 10848
+  },
+  "4": {
+   "test": 3,
+   "train": 16,
+   "inner_val": 5,
+   "test_groups": {
+    "mild": 3
+   },
+   "alpha_genes_estimated": 10830
+  }
+ },
+ "checks": {}
+}